I also reported this once for the IJsselmeer. The answer at that time was that the multi-polygon might not be correct. AFAIK the "map maker" at that time who left MNF, mentioned that.

The "current" answer that "some features are not displayed in high zoom" is very unlikely to me. The Ijsselmeer is a huge water mass compared to the whole Netherlands map. Features disappearing are small map "items", not the large ones.

If, instead of the Ijsselmeer, part of the entire western side of the Netherlands would disappear, would that also be a "some features are not displayed in high zoom"?

Currently it is only MNF doing this for already 1½ years or so. OsmAnd, MagiEarth and other OSM nav apps do display the IJsselmeer without issues.